There was speculation that this change also meant that Google has changed how they handle subdomains for ranking purposes. That is not true.

Googler, Pierre Far said in a Google + post that this is not true. He said it is only related to reporting within Google Webmaster Tools and not for how Google handles ranking.

Let me quote Pierre:

Dear webmasters: A lot of people have seen the recent announcement about the recent reorganization of backlinks in Webmaster Tools and are saying it's a reflection of a new way that Google handles links for ranking purposes.

Wrong.

This change is only for how Webmaster Tools displays link data to help webmasters understand their links a bit better. The most common use case is for links to both www and non-www versions of the same site, even if these two different hostnames are canonicalized correctly. Previously, Webmaster Tools considered the links to each separately even though webmasters (and everyone else) considered them to be the same site. That situation was not ideal and so this change helps simplify things quite a bit.